Many organic farmers are hopping mad at the U.S. Food and Drug Administration, and their reason involves perhaps the most underappreciated part of agriculture: plant food, aka fertilizer. Specifically, the FDA, as part of its overhaul of food safety regulations, wants to limit the use of animal manure.

"We think of it as the best thing in the world," says organic farmer Jim Crawford, "and they think of it as toxic and nasty and disgusting."

Every highly productive farmer depends on fertilizer. But organic farmers are practically obsessive about it, because they've renounced industrial sources of nutrients.

So on this crisp fall morning, Crawford is rhapsodic as he watches his field manager, Pearl Wetherall, spread manure across a field where cabbage grew last summer.

"All that green material — that cover crop and the cabbage — all mixed up with that nice black manure that's just rich and full of good microorganisms, and we're going to get a wonderful fertility situation for next spring here," he says.

Crawford, founder of New Morning Farm in south-central Pennsylvania, buys hundreds of tons of manure every year from a big turkey farm a few miles away. "It's really at the heart of our operation for having good, rich soil, and good fertility, so that we have the highest-quality crops."

It's also part of a natural cycle, and the basis of organic farming. Most crops strip vital nutrients from the soil. But the nutrients don't disappear; if you feed those crops to cattle or turkeys, the nutrients mostly end up in manure. For the turkey farmer, the manure is waste. For Crawford, it's precious. "Cycling nutrients. That's what it's all about. Cycling organic nutrients."

This is a typical practice among organic farmers, especially the smaller ones. But they may now have to change.

The Food and Drug Administration considers manure a food safety risk. Disease-causing microbes, such as salmonella or toxic forms of E. coli, are commonly found in animal waste.

Patricia Millner, a microbiologist with the U.S. Department of Agriculture's research center in Beltsville, Md., says scientists are now trying to figure out exactly how long such bacteria survive in the soil. "In some cases, salmonella will survive for a few weeks; in other cases, it'll be reported that it survives for 300-plus days," she says.

When they survive, microbes do get on food. Carrots or radishes, of course, grow right in the soil. But bacteria also end up on salad greens. Raindrops, for instance, splash soil and microbes onto the plants.

There's a lot of uncertainty about exactly how big of a risk this is. But the FDA is saying better safe than sorry.

The agency is proposing new national food safety rules. If those rules are enacted, when farmers spread raw manure on a field, they won't be allowed to harvest any crops from that field for the next nine months. (This applies only to crops that people eat raw, such as carrots or lettuce.)

The rules don't cover the smallest farms. They apply to farms with more than half a million dollars in annual sales, or which supply food to supermarkets.

But that includes Crawford's farm.

He already follows the organic rules; he doesn't harvest crops within four months of spreading manure. But having to wait nine months — longer than a growing season — would completely disrupt his operations. "We wouldn't even be able to function," he says.

There is an alternative: composted manure. The heat from composting kills disease-causing microbes. But Crawford says compost would cost him anywhere from three to six times more than manure. And he just doesn't see why he should have to switch, because he doesn't believe that what he does now is at all risky.

"No one's ever been sickened by anything we've grown, in probably millions of transactions between us and our customers over 40 years," he says. Crawford sells most of his food at farmers markets in Washington, D.C.

Yet organic farmers are not united in their opposition to the FDA regulations. There's a divide between large and small producers.

Earthbound Farm, in California, is among the biggest organic producers of salad greens. Will Daniel, the company's chief food integrity officer, says, "History is not always your greatest ally, unfortunately. We never thought that we would see spinach or other produce involved in outbreaks." But in 2006, his company's spinach was linked to an outbreak of E. coli poisoning; 200 people got sick. Three died.

Raw manure was not the source of that outbreak. (There's evidence the E. coli could have come from wild pigs that got into the fields.) But Daniel says using manure does involve risks that his company won't take.

"We've gone in that direction because we feel that it's very important to assure that we are not spreading these pathogens in our fields, that could lead to contaminated product," he says.

Daniel supports the FDA's proposed rules on manure. Many smaller organic farmers, meanwhile, are sending the FDA a blizzard of comments, arguing that the environmental benefits of using manure far outweigh the risks.

The comment period ends on Nov. 22.

Copyright 2014 NPR. To see more, visit http://www.npr.org/.

Transcript

STEVE INSKEEP, HOST:

It's MORNING EDITION, from NPR News. I'm Steve Inskeep.

RENEE MONTAGNE, HOST:

And I'm Renee Montagne. We're now going to spend a few minutes talking about where our food comes from and what nourishes those plants that, in turn, feed us. Every farmer uses fertilizer. Many organic farmers keep their fields fertile with manure from animals.

It's good for the environment, but the federal government now says there's a risk that it could make consumers sick. New rules would restrict the use of manure but organic farmers are fighting back, as NPR's Dan Charles reports.

CHARLES: His field manager, Pearl Wetherall, is pulling a manure spreader across a field where cabbage grew last summer. For Crawford, this animal waste is not waste. It's black gold.

JIM CRAWFORD: It's the best thing in the world for creating fertility in a natural, biological way.

CHARLES: Crawford buys hundreds of tons of manure every year from a big turkey farm a few miles away.

CRAWFORD: It's just really at the heart of our whole operation for having good, rich soil and good fertility, so we have the highest-quality crops.

CHARLES: It's also part of a natural cycle, the basis of organic farming. Growing crops strips nutrients from the soil. But the nutrients don't disappear. If you feed those crops to cattle or turkeys, the nutrients mostly end up in manure. Crawford says the right thing to do is bring them back to the soil.

CHARLES: This is typical among organic farmers, especially the smaller ones. But now they may have to change, because the Food and Drug Administration considers manure a food safety risk. You can sometimes find nasty, disease-causing microbes in manure - salmonella, for instance.

Patricia Millner, a microbiologist with the U.S. Department of Agriculture in Beltsville, Maryland, says scientists are trying to figure out exactly how long such bacteria survive in the soil.

PATRICIA MILLNER: In some cases, salmonella will survive for a few weeks. And in other cases, it'll be reported that it survives 300-and-some days.

CHARLES: And when they survive, they do get on food. Carrots or radishes, of course, grow right in the soil. But bacteria also get on salad greens.

MILLNER: Rainfall, there's splash that splashes them onto the plants.

CHARLES: There's a lot of uncertainty about exactly how big of a risk this is. But the FDA is saying better safe than sorry. It's proposing new national food safety rules. And if those rules go into effect, when farmers spread raw manure on a field, for the next nine months, they won't be allowed to harvest any crops from that field that people eat raw, like carrots or lettuce.

The rules don't apply to really small farms. They apply to farms with more than half-a-million dollars in annual sales, or which supply food to supermarkets. But that includes Jim Crawford's farm. He says he already follows the organic rules. He doesn't harvest crops within four months of spreading manure. But having to wait nine months - longer than a growing season - would completely disrupt his operations.

CRAWFORD: We wouldn't even be able to function.

CHARLES: There is an alternative: Composted manure. The heat from composting kills disease-causing microbes. But compost is three to six times more expensive than manure, and Crawford doesn't see why he should switch. He just doesn't believe that what he does now is at all dangerous.

CRAWFORD: No one's ever been sickened by anything we've grown, and in probably, literally, millions of transactions between our customers and us over 40 years.

CHARLES: The organic produce industry is not united on this. There's a divide between big and small. Will Daniels is the chief food integrity officer for Earthbound Farm in California, which sells organic salad greens nationwide.

WILL DANIELS: History is not always your greatest ally, unfortunately. We never thought that, you know, we would see spinach or other produce involved in outbreaks.

CHARLES: But in 2006, Earthbound Farm's spinach was linked to an outbreak of disease. Two hundred people got sick. Three died.

Now, raw manure was not the source of that outbreak. But Will Daniels says it's a risk his company will not take.

DANIELS: Primarily, we use a pelletized, processed chicken manure product.

CHARLES: All the bacteria in that fertilizer have been killed with heat and pressure.

DANIELS: We've gone that direction because we feel that it's very important to assure that we are not spreading these pathogens out in our field that could lead to contaminated product.

CHARLES: Daniels supports the FDA's proposed rules on manure. Many smaller organic farmers, meanwhile, are sending the FDA a blizzard of comments, arguing that the environmental benefits of using it outweigh the risks. The comment period ends this week.